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Conserved domains on  [gi|6322110|ref|NP_012184|]
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gag-pol fusion protein [Saccharomyces cerevisiae S288C]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
pepsin_retropepsin_like super family cl11403
Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular ...
 286-462 9.01e-117

Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular and retroviral pepsin-like aspartate proteases. The cellular pepsin and pepsin-like enzymes are twice as long as their retroviral counterparts. The cellular pepsin-like aspartic proteases are found in mammals, plants, fungi and bacteria. These well known and extensively characterized enzymes include pepsins, chymosin, rennin, cathepsins, and fungal aspartic proteases. Several have long been known to be medically (rennin, cathepsin D and E, pepsin) or commercially (chymosin) important. The eukaryotic pepsin-like proteases contain two domains possessing similar topological features. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except in the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The eukaryotic pepsin-like proteases have two active site ASP residues with each N- and C-terminal lobe contributing one residue. While the fungal and mammalian pepsins are bilobal proteins, retropepsins function as dimers and the monomer resembles structure of the N- or C-terminal domains of eukaryotic enzyme. The active site motif (Asp-Thr/Ser-Gly-Ser) is conserved between the retroviral and eukaryotic proteases and between the N-and C-terminal of eukaryotic pepsin-like proteases. The retropepsin-like family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements; as well as eukaryotic DNA-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. Retropepsin is synthesized as part of the POL polyprotein that contains an aspartyl-protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A) and A2 (retropepsin family).


The actual alignment was detected with superfamily member pfam12384:

Pssm-ID: 472175  Cd Length: 177  Bit Score: 363.96  E-value: 9.01e-117
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110     286 VLTDLELESKDQQTLFIKTLPIVHYIAIPEMDNTAEKTIKIQNTKVKTLFDSGSPTSFIRRDIVELLKYEIYETPPLRFR 365
Cdd:pfam12384    1 VLADLELESKDHKKLFIKSLPIVHYIAIPEMDKTAEKHIKIKNTKIKTLFDSGSPTSFIRRDIVELLKLEIHDTPPLRFR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110     366 GFVATKSAVTSEAVTIDLKINDLQITLAAYILDNMDYQLLIGNPILRRYPKILHTVLNTRESPDSLKPKTYRSETVNNVR 445
Cdd:pfam12384   81 GFIATESATTSEAVTIDLKIDDLQINLAAYILDKMDYQLLIGNPILRRYPKILHTILNTKECPDALKPKAYHSENVNNVK 160

                          170
                   ....*....|....*..
gi 6322110     446 TYSAGNRGNPRNIKLSF 462
Cdd:pfam12384  161 AKSAGNRGNPRNIKLSF 177
Ty3_capsid pfam19259
Ty3 transposon capsid-like protein; This entry corresponds to the capsid protein found in the ...
 16-206 2.81e-93

Ty3 transposon capsid-like protein; This entry corresponds to the capsid protein found in the Ty3 transposons of yeast as well as other transposable elements.


:

Pssm-ID: 437091 [Multi-domain]  Cd Length: 197  Bit Score: 299.39  E-value: 2.81e-93
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110      16 LPVECLPNFPIQPSLTFRGRNDSHKLKNFISEIMLNMSMISWPNDASRIVYCRRHLLNPAAQWANDFVQEQGILEITFDT 95
Cdd:pfam19259    1 LHVETLPNFMIQVILPFRGRKDVLKLKSFISEIMLQMSMIFWPNDAERIVFCARHLTGPAAQWFHDFVQEQGILDATFDT 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110      96 FIQGLYQHFYKPPDINKIFNAITQLSEAKLGIERLNQRFRKIWDRMPPDFMTEKAAIMTYTRLLTKETYNIVRMHKPETL 175
Cdd:pfam19259   81 FIKAFKQHFYGKPDINKLFNDIVNLSEAKLGIERYNSHFNRLWDLLPPDFLSEKAAIMFYIRGLKPETYIIVRLAKPSTL 160

                          170       180       190
                   ....*....|....*....|....*....|....*..
gi 6322110     176 KDAMEEAYQTTALTERFFPGFE------LDADGDTII 206
Cdd:pfam19259  161 KEAMEIAYETIPYTERFSPTFTqnsktvLDADGDTIM 197
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 649-823 2.67e-84

RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template. RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and Caulimoviruses.


:

Pssm-ID: 238825  Cd Length: 177  Bit Score: 273.32  E-value: 2.67e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110   649 KFIVPSKSPCSSPVVLVPKKDGTFRLCVDYRTLNKATISDPFPLPRIDNLLSRIGNAQIFTTLDLHSGYHQIPMEPKDRY 728
Cdd:cd01647    1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110   729 KTAFVTPSGKYEYTVMPFGLVNAPSTFARYMADTFRDL--RFVNVYLDDILIFSESPEEHWKHLDTVLERLKNENLIVKK 806
Cdd:cd01647   81 KTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLlgDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNP 160

                        170
                 ....*....|....*..
gi 6322110   807 KKCKFASEETEFLGYSI 823
Cdd:cd01647  161 EKCEFGVPEVEFLGHIV 177
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 915-1034 4.96e-48

Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


:

Pssm-ID: 260006 [Multi-domain]  Cd Length: 121  Bit Score: 167.28  E-value: 4.96e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110   915 RLTTDASKDGIGAVLEEVDNKNKLvGVVGYFSKSLESAQKNYPAGELELLGIIKALHHFRYMLHGKHFTLRTDHISLLSL 994
Cdd:cd09274    1 ILETDASDYGIGAVLSQEDDDGKE-RPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYL 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 6322110   995 QNKNEPARRVQRWLDDLATYDFTLEYLAGPKNVVADAISR 1034
Cdd:cd09274   80 LTQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSR 119
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 1117-1177 2.43e-16

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.


:

Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 74.59  E-value: 2.43e-16
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6322110    1117 VPIKQQNAVMRLYHDHtlfGGHFGVTVTLAKISPIYYWPKLQHSIIQYIRTCVQCQLIKSH 1177
Cdd:pfam17921    1 VPKSLRKEILKEAHDS---GGHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKPS 58
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1193-1291 7.93e-12

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


:

Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 63.10  E-value: 7.93e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110    1193 GRWldiSMDFVTGLPPTSNNLNMILVVVDRFSKRAHFIATRKTLDATQLIDLLFRYIFSYHGFPRTITSDRDVRMTADKY 1272
Cdd:pfam00665    3 QLW---QGDFTYIRIPGGGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKAF 79

                           90
                   ....*....|....*....
gi 6322110    1273 QELTKRLGIKSTMSSANHP 1291
Cdd:pfam00665   80 REFLKDLGIKPSFSRPGNP 98
 
Name Accession Description Interval E-value
Peptidase_A2B pfam12384
Ty3 transposon peptidase; Ty3 is a gypsy-type, retrovirus-like, element found in the budding ...
 286-462 9.01e-117

Ty3 transposon peptidase; Ty3 is a gypsy-type, retrovirus-like, element found in the budding yeast. The Ty3 aspartyl protease is required for processing of the viral polyprotein into its mature species.


Pssm-ID: 152819  Cd Length: 177  Bit Score: 363.96  E-value: 9.01e-117
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110     286 VLTDLELESKDQQTLFIKTLPIVHYIAIPEMDNTAEKTIKIQNTKVKTLFDSGSPTSFIRRDIVELLKYEIYETPPLRFR 365
Cdd:pfam12384    1 VLADLELESKDHKKLFIKSLPIVHYIAIPEMDKTAEKHIKIKNTKIKTLFDSGSPTSFIRRDIVELLKLEIHDTPPLRFR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110     366 GFVATKSAVTSEAVTIDLKINDLQITLAAYILDNMDYQLLIGNPILRRYPKILHTVLNTRESPDSLKPKTYRSETVNNVR 445
Cdd:pfam12384   81 GFIATESATTSEAVTIDLKIDDLQINLAAYILDKMDYQLLIGNPILRRYPKILHTILNTKECPDALKPKAYHSENVNNVK 160

                          170
                   ....*....|....*..
gi 6322110     446 TYSAGNRGNPRNIKLSF 462
Cdd:pfam12384  161 AKSAGNRGNPRNIKLSF 177
Ty3_capsid pfam19259
Ty3 transposon capsid-like protein; This entry corresponds to the capsid protein found in the ...
 16-206 2.81e-93

Ty3 transposon capsid-like protein; This entry corresponds to the capsid protein found in the Ty3 transposons of yeast as well as other transposable elements.


Pssm-ID: 437091 [Multi-domain]  Cd Length: 197  Bit Score: 299.39  E-value: 2.81e-93
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110      16 LPVECLPNFPIQPSLTFRGRNDSHKLKNFISEIMLNMSMISWPNDASRIVYCRRHLLNPAAQWANDFVQEQGILEITFDT 95
Cdd:pfam19259    1 LHVETLPNFMIQVILPFRGRKDVLKLKSFISEIMLQMSMIFWPNDAERIVFCARHLTGPAAQWFHDFVQEQGILDATFDT 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110      96 FIQGLYQHFYKPPDINKIFNAITQLSEAKLGIERLNQRFRKIWDRMPPDFMTEKAAIMTYTRLLTKETYNIVRMHKPETL 175
Cdd:pfam19259   81 FIKAFKQHFYGKPDINKLFNDIVNLSEAKLGIERYNSHFNRLWDLLPPDFLSEKAAIMFYIRGLKPETYIIVRLAKPSTL 160

                          170       180       190
                   ....*....|....*....|....*....|....*..
gi 6322110     176 KDAMEEAYQTTALTERFFPGFE------LDADGDTII 206
Cdd:pfam19259  161 KEAMEIAYETIPYTERFSPTFTqnsktvLDADGDTIM 197
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 649-823 2.67e-84

RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template. RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and Caulimoviruses.


Pssm-ID: 238825  Cd Length: 177  Bit Score: 273.32  E-value: 2.67e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110   649 KFIVPSKSPCSSPVVLVPKKDGTFRLCVDYRTLNKATISDPFPLPRIDNLLSRIGNAQIFTTLDLHSGYHQIPMEPKDRY 728
Cdd:cd01647    1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110   729 KTAFVTPSGKYEYTVMPFGLVNAPSTFARYMADTFRDL--RFVNVYLDDILIFSESPEEHWKHLDTVLERLKNENLIVKK 806
Cdd:cd01647   81 KTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLlgDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNP 160

                        170
                 ....*....|....*..
gi 6322110   807 KKCKFASEETEFLGYSI 823
Cdd:cd01647  161 EKCEFGVPEVEFLGHIV 177
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 915-1034 4.96e-48

Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260006 [Multi-domain]  Cd Length: 121  Bit Score: 167.28  E-value: 4.96e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110   915 RLTTDASKDGIGAVLEEVDNKNKLvGVVGYFSKSLESAQKNYPAGELELLGIIKALHHFRYMLHGKHFTLRTDHISLLSL 994
Cdd:cd09274    1 ILETDASDYGIGAVLSQEDDDGKE-RPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYL 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 6322110   995 QNKNEPARRVQRWLDDLATYDFTLEYLAGPKNVVADAISR 1034
Cdd:cd09274   80 LTQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSR 119
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 665-823 6.37e-47

Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.


Pssm-ID: 395031 [Multi-domain]  Cd Length: 189  Bit Score: 166.71  E-value: 6.37e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110     665 VPKKD-GTFRLC----VDYRTLNKATI-------SDPFPLPRIDNLLSRIGNAQIFTTLDLHSGYHQIPMEPKDRYKTAF 732
Cdd:pfam00078    1 IPKKGkGKYRPIsllsIDYKALNKIIVkrlkpenLDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110     733 VTPS-----------GKYEYTVMPFGLVNAPSTFARYMADTFRDLR-----FVNVYLDDILIFSESPEEHWKHLDTVLER 796
Cdd:pfam00078   81 TTPPininwngelsgGRYEWKGLPQGLVLSPALFQLFMNELLRPLRkraglTLVRYADDILIFSKSEEEHQEALEEVLEW 160

                          170       180
                   ....*....|....*....|....*....
gi 6322110     797 LKNENLIVKKKKCKFA--SEETEFLGYSI 823
Cdd:pfam00078  161 LKESGLKINPEKTQFFlkSKEVKYLGVTL 189
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
884-984 2.64e-37

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 135.70  E-value: 2.64e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110     884 WTEKQDKAIEKLKAALCNSPVLVPFNNKANYRLTTDASKDGIGAVLEEVDNKNKLVgVVGYFSKSLESAQKNYPAGELEL 963
Cdd:pfam17919    1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLSQEDDDGGER-PIAYASRKLSPAERNYSTTEKEL 79

                           90       100
                   ....*....|....*....|.
gi 6322110     964 LGIIKALHHFRYMLHGKHFTL 984
Cdd:pfam17919   80 LAIVFALKKFRHYLLGRKFTV 100
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 1117-1177 2.43e-16

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.


Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 74.59  E-value: 2.43e-16
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6322110    1117 VPIKQQNAVMRLYHDHtlfGGHFGVTVTLAKISPIYYWPKLQHSIIQYIRTCVQCQLIKSH 1177
Cdd:pfam17921    1 VPKSLRKEILKEAHDS---GGHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKPS 58
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 323-412 2.77e-16

Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements, as well as eukaryotic dna-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133136  Cd Length: 92  Bit Score: 75.45  E-value: 2.77e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110   323 TIKIQNTKVKTLFDSGSPTSFIRRDIVELLKYE-IYETPPLRFRGFVATKSAVTSEAVTIDLKINDLQITLAAYILDNMD 401
Cdd:cd00303    2 KGKINGVPVRALVDSGASVNFISESLAKKLGLPpRLLPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDLLS 81

                         90
                 ....*....|.
gi 6322110   402 YQLLIGNPILR 412
Cdd:cd00303   82 YDVILGRPWLE 92
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1193-1291 7.93e-12

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 63.10  E-value: 7.93e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110    1193 GRWldiSMDFVTGLPPTSNNLNMILVVVDRFSKRAHFIATRKTLDATQLIDLLFRYIFSYHGFPRTITSDRDVRMTADKY 1272
Cdd:pfam00665    3 QLW---QGDFTYIRIPGGGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKAF 79

                           90
                   ....*....|....*....
gi 6322110    1273 QELTKRLGIKSTMSSANHP 1291
Cdd:pfam00665   80 REFLKDLGIKPSFSRPGNP 98
transpos_IS481 NF033577
IS481 family transposase; null
 1216-1344 2.35e-06

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 51.05  E-value: 2.35e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110   1216 ILVVVDRFSKRA-HFIATRKTLDATqlIDLLFRyIFSYHGFP-RTITSDRDVRMTADK--YQELTKRLGIKSTMSSANHP 1291
Cdd:NF033577  149 LHTAIDDHSRFAyAELYPDETAETA--ADFLRR-AFAEHGIPiRRVLTDNGSEFRSRAhgFELALAELGIEHRRTRPYHP 225

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 6322110   1292 QTDGQSERTIQTL-NRLLRAYVSTNIQNWHVYLPQIEFVYNST-PTRTL-GKSPFE 1344
Cdd:NF033577  226 QTNGKVERFHRTLkDEFAYARPYESLAELQAALDEWLHHYNHHrPHSALgGKTPAE 281
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
1216-1353 2.61e-05

Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 47.84  E-value: 2.61e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110  1216 ILVVVDRFSKRAHFIATRKTLDATQLIDLLFRYIFSYHGF-PRTITSDRDVRMTADKYQELTKRLGIKSTMSSANHPQTD 1294
Cdd:COG2801  168 LAAVIDLFSREIVGWSVSDSMDAELVVDALEMAIERRGPPkPLILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDN 247

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 6322110  1295 GQSERTIQTL-NRLLRAYVSTN-------IQNWhvylpqIEFvYNST-PTRTLG-KSPFEIDLGYLPNT 1353
Cdd:COG2801  248 AFIESFFGTLkYELLYRRRFESleeareaIEEY------IEF-YNHErPHSSLGyLTPAEYEKQLAAAA 309
 
Name Accession Description Interval E-value
Peptidase_A2B pfam12384
Ty3 transposon peptidase; Ty3 is a gypsy-type, retrovirus-like, element found in the budding ...
 286-462 9.01e-117

Ty3 transposon peptidase; Ty3 is a gypsy-type, retrovirus-like, element found in the budding yeast. The Ty3 aspartyl protease is required for processing of the viral polyprotein into its mature species.


Pssm-ID: 152819  Cd Length: 177  Bit Score: 363.96  E-value: 9.01e-117
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110     286 VLTDLELESKDQQTLFIKTLPIVHYIAIPEMDNTAEKTIKIQNTKVKTLFDSGSPTSFIRRDIVELLKYEIYETPPLRFR 365
Cdd:pfam12384    1 VLADLELESKDHKKLFIKSLPIVHYIAIPEMDKTAEKHIKIKNTKIKTLFDSGSPTSFIRRDIVELLKLEIHDTPPLRFR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110     366 GFVATKSAVTSEAVTIDLKINDLQITLAAYILDNMDYQLLIGNPILRRYPKILHTVLNTRESPDSLKPKTYRSETVNNVR 445
Cdd:pfam12384   81 GFIATESATTSEAVTIDLKIDDLQINLAAYILDKMDYQLLIGNPILRRYPKILHTILNTKECPDALKPKAYHSENVNNVK 160

                          170
                   ....*....|....*..
gi 6322110     446 TYSAGNRGNPRNIKLSF 462
Cdd:pfam12384  161 AKSAGNRGNPRNIKLSF 177
Ty3_capsid pfam19259
Ty3 transposon capsid-like protein; This entry corresponds to the capsid protein found in the ...
 16-206 2.81e-93

Ty3 transposon capsid-like protein; This entry corresponds to the capsid protein found in the Ty3 transposons of yeast as well as other transposable elements.


Pssm-ID: 437091 [Multi-domain]  Cd Length: 197  Bit Score: 299.39  E-value: 2.81e-93
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110      16 LPVECLPNFPIQPSLTFRGRNDSHKLKNFISEIMLNMSMISWPNDASRIVYCRRHLLNPAAQWANDFVQEQGILEITFDT 95
Cdd:pfam19259    1 LHVETLPNFMIQVILPFRGRKDVLKLKSFISEIMLQMSMIFWPNDAERIVFCARHLTGPAAQWFHDFVQEQGILDATFDT 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110      96 FIQGLYQHFYKPPDINKIFNAITQLSEAKLGIERLNQRFRKIWDRMPPDFMTEKAAIMTYTRLLTKETYNIVRMHKPETL 175
Cdd:pfam19259   81 FIKAFKQHFYGKPDINKLFNDIVNLSEAKLGIERYNSHFNRLWDLLPPDFLSEKAAIMFYIRGLKPETYIIVRLAKPSTL 160

                          170       180       190
                   ....*....|....*....|....*....|....*..
gi 6322110     176 KDAMEEAYQTTALTERFFPGFE------LDADGDTII 206
Cdd:pfam19259  161 KEAMEIAYETIPYTERFSPTFTqnsktvLDADGDTIM 197
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 649-823 2.67e-84

RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template. RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and Caulimoviruses.


Pssm-ID: 238825  Cd Length: 177  Bit Score: 273.32  E-value: 2.67e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110   649 KFIVPSKSPCSSPVVLVPKKDGTFRLCVDYRTLNKATISDPFPLPRIDNLLSRIGNAQIFTTLDLHSGYHQIPMEPKDRY 728
Cdd:cd01647    1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110   729 KTAFVTPSGKYEYTVMPFGLVNAPSTFARYMADTFRDL--RFVNVYLDDILIFSESPEEHWKHLDTVLERLKNENLIVKK 806
Cdd:cd01647   81 KTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLlgDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNP 160

                        170
                 ....*....|....*..
gi 6322110   807 KKCKFASEETEFLGYSI 823
Cdd:cd01647  161 EKCEFGVPEVEFLGHIV 177
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 915-1034 4.96e-48

Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260006 [Multi-domain]  Cd Length: 121  Bit Score: 167.28  E-value: 4.96e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110   915 RLTTDASKDGIGAVLEEVDNKNKLvGVVGYFSKSLESAQKNYPAGELELLGIIKALHHFRYMLHGKHFTLRTDHISLLSL 994
Cdd:cd09274    1 ILETDASDYGIGAVLSQEDDDGKE-RPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYL 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 6322110   995 QNKNEPARRVQRWLDDLATYDFTLEYLAGPKNVVADAISR 1034
Cdd:cd09274   80 LTQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSR 119
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 665-823 6.37e-47

Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.


Pssm-ID: 395031 [Multi-domain]  Cd Length: 189  Bit Score: 166.71  E-value: 6.37e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110     665 VPKKD-GTFRLC----VDYRTLNKATI-------SDPFPLPRIDNLLSRIGNAQIFTTLDLHSGYHQIPMEPKDRYKTAF 732
Cdd:pfam00078    1 IPKKGkGKYRPIsllsIDYKALNKIIVkrlkpenLDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110     733 VTPS-----------GKYEYTVMPFGLVNAPSTFARYMADTFRDLR-----FVNVYLDDILIFSESPEEHWKHLDTVLER 796
Cdd:pfam00078   81 TTPPininwngelsgGRYEWKGLPQGLVLSPALFQLFMNELLRPLRkraglTLVRYADDILIFSKSEEEHQEALEEVLEW 160

                          170       180
                   ....*....|....*....|....*....
gi 6322110     797 LKNENLIVKKKKCKFA--SEETEFLGYSI 823
Cdd:pfam00078  161 LKESGLKINPEKTQFFlkSKEVKYLGVTL 189
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
884-984 2.64e-37

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 135.70  E-value: 2.64e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110     884 WTEKQDKAIEKLKAALCNSPVLVPFNNKANYRLTTDASKDGIGAVLEEVDNKNKLVgVVGYFSKSLESAQKNYPAGELEL 963
Cdd:pfam17919    1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLSQEDDDGGER-PIAYASRKLSPAERNYSTTEKEL 79

                           90       100
                   ....*....|....*....|.
gi 6322110     964 LGIIKALHHFRYMLHGKHFTL 984
Cdd:pfam17919   80 LAIVFALKKFRHYLLGRKFTV 100
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 914-1012 1.14e-33

RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) activities allow reverse transcriptases to convert the single-stranded retroviral RNA genome into double-stranded DNA, which is integrated into the host chromosome during infection. This entry represents the RNase H like domain.


Pssm-ID: 465565  Cd Length: 104  Bit Score: 125.32  E-value: 1.14e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110     914 YRLTTDASKDGIGAVLEEVDNKNKLvGVVGYFSKSLESAQKNYPAGELELLGIIKALHHFRYMLHGKHFTLRTDHISLLS 993
Cdd:pfam17917    6 FILETDASDYGIGAVLSQKDEDGKE-RPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDHKPLKY 84

                           90
                   ....*....|....*....
gi 6322110     994 LQNKNEPARRVQRWLDDLA 1012
Cdd:pfam17917   85 LFTPKELNGRLARWALFLQ 103
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 622-823 6.05e-30

RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. Phylogenetic analysis suggests that ZFERV belongs to a distinct group of retroviruses.


Pssm-ID: 239685 [Multi-domain]  Cd Length: 210  Bit Score: 118.60  E-value: 6.05e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110   622 LPRLQPYHVTEKNEQEINKIVQKLLDNKFIVPSKSPCSSPVVLVPKKDG-TFRLCVDYRTLNKATISDPFPLPRIDNLLS 700
Cdd:cd03715    1 PVNQKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGnDYRMVQDLRLVNQAVLPIHPAVPNPYTLLS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110   701 RIGNA-QIFTTLDLHSGYHQIPMEPKDRYKTAFVTPSGKYEYTVMPFGLVNAPSTFARYMAdtfRDLRFVNV-------- 771
Cdd:cd03715   81 LLPPKhQWYTVLDLANAFFSLPLAPDSQPLFAFEWEGQQYTFTRLPQGFKNSPTLFHEALA---RDLAPFPLehegtill 157

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 6322110   772 -YLDDILIFSESPEEHWKHLDTVLERLKNENLIVKKKKCKFASEETEFLGYSI 823
Cdd:cd03715  158 qYVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLGVVW 210
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 623-823 8.48e-26

RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.


Pssm-ID: 238823 [Multi-domain]  Cd Length: 213  Bit Score: 106.98  E-value: 8.48e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110   623 PRLQPYHVTEKNEQEINKIVQKLLDNKFIVPSKSPCSSPVVLVPKKDGTFRLCVDYRTLNKATIsdPF-------PLPri 695
Cdd:cd01645    2 VWIKQWPLTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQ--DMgalqpglPHP-- 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110   696 dnllSRIGNAQIFTTLDLHSGYHQIPMEPKDRYKTAF-------VTPSGKYEYTVMPFGLVNAPSTFARYMADTFRDLR- 767
Cdd:cd01645   78 ----AALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFtvpsinnKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRk 153

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6322110   768 -----FVNVYLDDILIFSESPEEHWKHLDTVLERLKNENLIVKKKKCKfASEETEFLGYSI 823
Cdd:cd01645  154 qypdiVIYHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQ-KEPPFQYLGYEL 213
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 1117-1177 2.43e-16

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.


Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 74.59  E-value: 2.43e-16
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6322110    1117 VPIKQQNAVMRLYHDHtlfGGHFGVTVTLAKISPIYYWPKLQHSIIQYIRTCVQCQLIKSH 1177
Cdd:pfam17921    1 VPKSLRKEILKEAHDS---GGHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKPS 58
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 323-412 2.77e-16

Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements, as well as eukaryotic dna-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133136  Cd Length: 92  Bit Score: 75.45  E-value: 2.77e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110   323 TIKIQNTKVKTLFDSGSPTSFIRRDIVELLKYE-IYETPPLRFRGFVATKSAVTSEAVTIDLKINDLQITLAAYILDNMD 401
Cdd:cd00303    2 KGKINGVPVRALVDSGASVNFISESLAKKLGLPpRLLPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDLLS 81

                         90
                 ....*....|.
gi 6322110   402 YQLLIGNPILR 412
Cdd:cd00303   82 YDVILGRPWLE 92
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1193-1291 7.93e-12

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 63.10  E-value: 7.93e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110    1193 GRWldiSMDFVTGLPPTSNNLNMILVVVDRFSKRAHFIATRKTLDATQLIDLLFRYIFSYHGFPRTITSDRDVRMTADKY 1272
Cdd:pfam00665    3 QLW---QGDFTYIRIPGGGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKAF 79

                           90
                   ....*....|....*....
gi 6322110    1273 QELTKRLGIKSTMSSANHP 1291
Cdd:pfam00665   80 REFLKDLGIKPSFSRPGNP 98
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 711-820 1.44e-10

RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members of the subfamily include the Dictyostelium DIRS-1, Volvox carteri kangaroo, and Panagrellus redivivus PAT elements. These elements differ from LTR and conventional non-LTR retrotransposons. They contain split direct repeat (SDR) termini, and have been proposed to integrate via double-stranded closed-circle DNA intermediates assisted by an encoded recombinase which is similar to gamma-site-specific integrase.


Pssm-ID: 239684 [Multi-domain]  Cd Length: 119  Bit Score: 60.05  E-value: 1.44e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110   711 LDLHSGYHQIPMEPKDRYKTAFVTPSGKYEYTVMPFGLVNAPSTFARYMADTFRDLRFVNV----YLDDILIFSESPeeh 786
Cdd:cd03714    1 VDLKDAYFHIPILPRSRDLLGFAWQGETYQFKALPFGLSLAPRVFTKVVEALLAPLRLLGVrifsYLDDLLIIASSI--- 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 6322110   787 wKHLDTVLERLK-----NENLIVKKKKCK-FASEETEFLG 820
Cdd:cd03714   78 -KTSEAVLRHLRatllaNLGFTLNLEKSKlGPTQRITFLG 116
RNase_HI_RT_DIRS1 cd09275
DIRS1 family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 915-1035 1.12e-09

DIRS1 family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. The structural features of DIRS1-group elements are different from typical LTR elements. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260007  Cd Length: 120  Bit Score: 57.68  E-value: 1.12e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110   915 RLTTDASKDGIGAVLEEVDNKnklvgvvGYFSKSlesaQKNYPAGELELLGIIKALHHFRYMLHGKHFTLRTDHISLLSL 994
Cdd:cd09275    1 VLFTDASLSGWGAYLLNSRAH-------GPWSAD----ERNKHINLLELKAVLLALQHFAAELKNRKILIRTDNTTAVAY 69

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 6322110   995 QNK---------NEPARRVQRWLDDLATYdFTLEYLAGPKNVVADAISRA 1035
Cdd:cd09275   70 INKqggtsspplLALARQILLWCEQRNIW-LRASHIPGVLNTEADRLSRL 118
transpos_IS481 NF033577
IS481 family transposase; null
 1216-1344 2.35e-06

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 51.05  E-value: 2.35e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110   1216 ILVVVDRFSKRA-HFIATRKTLDATqlIDLLFRyIFSYHGFP-RTITSDRDVRMTADK--YQELTKRLGIKSTMSSANHP 1291
Cdd:NF033577  149 LHTAIDDHSRFAyAELYPDETAETA--ADFLRR-AFAEHGIPiRRVLTDNGSEFRSRAhgFELALAELGIEHRRTRPYHP 225

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 6322110   1292 QTDGQSERTIQTL-NRLLRAYVSTNIQNWHVYLPQIEFVYNST-PTRTL-GKSPFE 1344
Cdd:NF033577  226 QTNGKVERFHRTLkDEFAYARPYESLAELQAALDEWLHHYNHHrPHSALgGKTPAE 281
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
1216-1353 2.61e-05

Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 47.84  E-value: 2.61e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110  1216 ILVVVDRFSKRAHFIATRKTLDATQLIDLLFRYIFSYHGF-PRTITSDRDVRMTADKYQELTKRLGIKSTMSSANHPQTD 1294
Cdd:COG2801  168 LAAVIDLFSREIVGWSVSDSMDAELVVDALEMAIERRGPPkPLILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDN 247

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 6322110  1295 GQSERTIQTL-NRLLRAYVSTN-------IQNWhvylpqIEFvYNST-PTRTLG-KSPFEIDLGYLPNT 1353
Cdd:COG2801  248 AFIESFFGTLkYELLYRRRFESleeareaIEEY------IEF-YNHErPHSSLGyLTPAEYEKQLAAAA 309
gag-asp_proteas pfam13975
gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is ...
 323-413 2.73e-04

gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is found pre-dominantly in retroviral proteins.


Pssm-ID: 464060  Cd Length: 92  Bit Score: 41.41  E-value: 2.73e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110     323 TIKIQNTKVKTLFDSGSPTSFIRRDIVELLKYEIyetPPLRFRGFVATKS-AVTSEAVTID-LKINDLQIT-LAAYILDN 399
Cdd:pfam13975    2 DVTINGRPVRFLVDTGASVTVISEALAERLGLDR---LVDAYPVTVRTANgTVRAARVRLDsVKIGGIELRnVPAVVLPG 78

                           90
                   ....*....|....
gi 6322110     400 MDYQLLIGNPILRR 413
Cdd:pfam13975   79 DLDDVLLGMDFLKR 92
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 70-157 1.38e-03

Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.


Pssm-ID: 367628  Cd Length: 97  Bit Score: 39.62  E-value: 1.38e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110      70 HLLNPAAQWANDFVQEQGILEITFDTFIQGLYQHFYKPPDINKIFNAITQLSEAKLGIERLNQRFRKIWDRMPPDFMTEK 149
Cdd:pfam03732    6 SLRGAALTWWKSLVARSIDAFDSWDELKDAFLKRFFPSIRKDLLRNELRSLRQGTESVREYVERFKRLARQLPHHGRDEE 85


                   ....*...
gi 6322110     150 AAIMTYTR 157
Cdd:pfam03732   86 ALISAFLR 93
RP_DDI cd05479
RP_DDI; retropepsin-like domain of DNA damage inducible protein; The family represents the ...
 324-414 5.38e-03

RP_DDI; retropepsin-like domain of DNA damage inducible protein; The family represents the retropepsin-like domain of DNA damage inducible protein. DNA damage inducible protein has a retropepsin-like domain and an amino-terminal ubiquitin-like domain and/or a UBA (ubiquitin-associated) domain. This CD represents the retropepsin-like domain of DDI.


Pssm-ID: 133146  Cd Length: 124  Bit Score: 38.30  E-value: 5.38e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110   324 IKIQNTKVKTLFDSGSPTSFIRRDIVE------LLKYeiyetpplRFRGfVAtKSAVTSEAV----TIDLKINDLQITLA 393
Cdd:cd05479   21 VEINGVPVKAFVDSGAQMTIMSKACAEkcglmrLIDK--------RFQG-IA-KGVGTQKILgrihLAQVKIGNLFLPCS 90

                         90       100
                 ....*....|....*....|.
gi 6322110   394 AYILDNMDYQLLIGNPILRRY 414
Cdd:cd05479   91 FTVLEDDDVDFLIGLDMLKRH 111
RT_Bac_retron_I cd01646
RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
 757-821 8.25e-03

RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.


Pssm-ID: 238824 [Multi-domain]  Cd Length: 158  Bit Score: 38.85  E-value: 8.25e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322110   757 RYMADTFRDLRFVNvYLDDILIFSESPEEHWKHLDTVLERLKNENLIVKKKKCK-----FASEETEFLGY 821
Cdd:cd01646   74 HELKSKLKGVDYVR-YVDDIRIFADSKEEAEEILEELKEFLAELGLSLNLSKTEilplpEGTASKDFLGY 142
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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